Configuring graph-based tracks

Genome Browser graph-based tracks may be configured in a variety of ways to highlight different aspects of the displayed information. Some track types, such as BAM tracks and certain gene tracks, offer dynamic calculation of items in the current window to display a density graph where the height is proportional to the number of items mapped to each genomic position. The following information explains each of the available configuration options.

Overlay method: The default "transparent" setting displays the colored transparent graphs of multiple subtracks overlayed in the same vertical space. The "solid" setting displays the colored opaque graphs of multiple subtracks overlayed in the same vertical space. The "stacked" setting displays each graph stacked on top of each other where the high point of the graph is the sum of all the values. The "none" setting displays each graph in its own vertical space. Note that not all graph-based tracks include this option.

Type of graph: The default "Bar" setting depicts the graph data using color-filled bars. To view the data as a series of points or lines, select the "Points" setting.

Track height: To change the default display height of the graph in pixels, type in a value from within the indicated range.

Vertical viewing range: The min and max values specify the vertical portion of the graph that is displayed (default range is 30-70). These numbers can be used to set data threshold indicators. For example, to display only those GC values greater than 50 percent, set the min value to "50".

Data view scaling: The default "Use vertical viewing range setting" option displays the data using the parameters specified in the Vertical viewing range setting. To configure the graph to automatically scale to a range defined by the minimum and maximum data points in the current view, select the "Auto-scale to data view" option. To keep the y=0 value in view at all times when Auto-scale is selected, set "Always include zero" to "ON".

Transform function: Transforms the data points by the function selected in the drop-down menu. Usually the default setting is "None".

Windowing function: When a view is too large to show individual data values, the values must be combined to produce a plot point. This option specifies the combining function to be used (default is "Mean"):

• "Mean+whiskers" - displays the mean in a dark shade, one standard deviation around the mean in a medium shade, and the maximum/minimum in a light shade. For bar graphs only the mean, the mean plus a standard deviation, and the max are visible. This mode is not available if the Overlay method is stacked.
• "Maximum" - displays the maximum value of all the points to be combined
• "Mean" - displays the mean
• "Minimum" - displays the minimum of all the points to be combined

Smoothing window: When set to a numerical value, this option determines the size, in pixels, of a smoothing window to be passed over the plot to smooth the edges of the bars or lines. This is equivalent to a trend line calculation on the graph. The default setting is "OFF".

Negate values: When checked, all values in the wiggle are negated, meaning that positive values become negative and vice-versa. This is useful for wiggles representing transcription or other activities on the Crick strand. Be aware that wiggles with negative values are drawn in altColor not color as positive values e.

Draw indicator lines:

• at y=0.0: Select the "ON" setting to display a line marking the 0.0 position on the graph (default is "OFF").
• at y= : Select the "ON" setting to display a line on the graph at the specified numerical value (defaults are "0" and "OFF"). This line can be used to mark a significant threshold on the graph.

When you have finished making your configuration changes, click the Apply button to preview your changes, or click the Submit button to return to the annotation track display page.